Library & Dataset

Using OLR

Inspect Dataset Using Training and Validation

OLR Equations

Inspect Dataset Using Training and Validation

#vclust <- varclus (~ angle + building+EN +TC + TC_mature_Soil + TC_saprolito +  TC_weath_rock + TC_rock + TC_geol_desfav + Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte + DepTaludeAterro + landfill + garbage + construction_deposit + crack + leaning_wall + scars + downward_floor + tilted + fracture + conc_rainfall_water + wastewater + leak + septic_tank + drainage + tree + ground_veg + deforestation + banana , data=train.data)

# took out density since training has 0 d4 and it was not allowing do the plot

#p <- plot(vclust)
par(mfrow=c(8,4))
plot.xmean.ordinaly (risk~  angle+ density+building+EN +TC + TC_mature_Soil + TC_saprolito +  TC_weath_rock + TC_rock + TC_geol_desfav + Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte + DepTaludeAterro + landfill + garbage + construction_deposit + crack + leaning_wall + scars + downward_floor + tilted + fracture + conc_rainfall_water + wastewater + leak + septic_tank  + tree + ground_veg + deforestation + banana + drainage, data=train.data, cr=TRUE , subn=FALSE , cex.points =0.65)

#angle + building+density+EN +TC + TC_mature_Soil + TC_saprolito +  TC_weath_rock + TC_rock + TC_geol_desfav + Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte + DepTaludeAterro + aterro + lixo + entulho + crack + belly_wall + scars + drawback + tilted + fracture + conc_rainfall_water + wastewater + leak + septic_tank + drainage + tree + ground_veg + deforestation + banana 

Diagnostic 2: Proportion (-5% of one of the parameters based on what is expected. Since some parameters have 2 predictors, others 5)

#library(plyr)
angle <- count(train.data$angle) # angle A less than 5% but the rest are okay (3,50, 91, 277, 109) Expected=106
angle <- angle %>%
  mutate("Percentage"=(freq/106)*100)%>%
  mutate("Classifier" = "angle")



building <- count(train.data$building) %>% #(445, 46, 39) 
  mutate ("Percentage"=(freq/176.7)*100)%>%
  mutate("Classifier" = "building")

density <- count(train.data$density)  %>% #(79, 415, 36) # d4 =0 
  mutate ("Percentage"=(freq/132.5)*100)%>%
  mutate("Classifier" = "density")


EN <- count(train.data$EN) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "EN")

TC <- count(train.data$TC)  %>%
  mutate ("Percentage"=(freq/265)*100) %>%
  mutate("Classifier" = "TC")

TC_MatureSoil <- count(train.data$TC_mature_Soil) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "TC_MatureSoil")


TC_Saprolito <- count(train.data$TC_saprolito)  %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "TC_Saprolito")

TC_WRock <- count(train.data$TC_weath_rock) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "TC_WRock")

TC_rock <- count(train.data$TC_rock) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "TC_rock")

TC_geol_desfav <- count(train.data$TC_geol_desfav) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "TC_geol_desfav")

Taterro <- count(train.data$Taterro) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "Taterro")

DepEncNatural <- count(train.data$DepEncNatural) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "TC")

DepTaludeAterro <- count(train.data$DepTaludeAterro) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "DepEncNatural")

DepTaludeCorte <- count(train.data$DepTaludeCorte) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "DepTaludeCorte")

DepTaludeAterro <- count(train.data$DepTaludeAterro) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "DepTaludeAterro")

construction_deposit <- count(train.data$construction_deposit) %>%
  mutate ("Percentage"=(freq/265)*100) %>%
  mutate("Classifier" = "construction_deposit")

garbage <- count(train.data$garbage) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "garbage")

crack <- count(train.data$crack) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "crack")

leaning_wall <- count(train.data$leaning_wall) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "leaning_wall")

scars <- count(train.data$scars) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "DepTaludeAterro")

downward_floor <- count(train.data$downward_floor) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "scars")

tilted <- count(train.data$tilted) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "tilted")

fracture <- count(train.data$fracture) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "fracture")

conc_rainfall_water <- count(train.data$conc_rainfall_water) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "DepTaludeAterro")

leak <- count(train.data$leak) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "conc_rainfall_water")

wastewater <- count(train.data$wastewater) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "wastewater")

septic_tank <- count(train.data$septic_tank) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "septic_tank")

drainage <- count(train.data$drainage) %>%
  mutate ("Percentage"=(freq/176.7)*100)%>%
  mutate("Classifier" = "drainage")

tree <- count(train.data$tree) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "tree")

ground_veg <- count(train.data$ground_veg) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "ground_veg")

deforestation <- count(train.data$deforestation) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "deforestation")

banana <- count(train.data$banana) %>%
  mutate ("Percentage"=(freq/265)*100)%>%
  mutate("Classifier" = "banana")


df <- rbind(TC, TC_MatureSoil, TC_Saprolito, TC_WRock, TC_rock, TC_geol_desfav, Taterro, DepEncNatural, DepTaludeAterro, DepTaludeCorte,construction_deposit, garbage, crack, leaning_wall, 
            scars, downward_floor, tilted, fracture, conc_rainfall_water, leak, wastewater, septic_tank, drainage, tree, ground_veg, deforestation, banana, 
            angle,
            building, density, EN
)

df
##        x freq  Percentage           Classifier
## 1  FALSE   46  17.3584906                   TC
## 2   TRUE  483 182.2641509                   TC
## 3  FALSE  274 103.3962264        TC_MatureSoil
## 4   TRUE  255  96.2264151        TC_MatureSoil
## 5  FALSE  451 170.1886792         TC_Saprolito
## 6   TRUE   78  29.4339623         TC_Saprolito
## 7  FALSE  518 195.4716981             TC_WRock
## 8   TRUE   11   4.1509434             TC_WRock
## 9  FALSE  528 199.2452830              TC_rock
## 10  TRUE    1   0.3773585              TC_rock
## 11 FALSE  517 195.0943396       TC_geol_desfav
## 12  TRUE   12   4.5283019       TC_geol_desfav
## 13 FALSE  469 176.9811321              Taterro
## 14  TRUE   60  22.6415094              Taterro
## 15 FALSE  395 149.0566038                   TC
## 16  TRUE  134  50.5660377                   TC
## 17 FALSE  510 192.4528302      DepTaludeAterro
## 18  TRUE   19   7.1698113      DepTaludeAterro
## 19 FALSE  310 116.9811321       DepTaludeCorte
## 20  TRUE  219  82.6415094       DepTaludeCorte
## 21 FALSE  322 121.5094340 construction_deposit
## 22  TRUE  207  78.1132075 construction_deposit
## 23 FALSE  355 133.9622642              garbage
## 24  TRUE  174  65.6603774              garbage
## 25 FALSE  444 167.5471698                crack
## 26  TRUE   85  32.0754717                crack
## 27 FALSE  497 187.5471698         leaning_wall
## 28  TRUE   32  12.0754717         leaning_wall
## 29 FALSE  322 121.5094340      DepTaludeAterro
## 30  TRUE  207  78.1132075      DepTaludeAterro
## 31 FALSE  469 176.9811321                scars
## 32  TRUE   60  22.6415094                scars
## 33 FALSE  433 163.3962264               tilted
## 34  TRUE   96  36.2264151               tilted
## 35 FALSE  528 199.2452830             fracture
## 36  TRUE    1   0.3773585             fracture
## 37 FALSE   23   8.6792453      DepTaludeAterro
## 38  TRUE  506 190.9433962      DepTaludeAterro
## 39 FALSE  345 130.1886792  conc_rainfall_water
## 40  TRUE  184  69.4339623  conc_rainfall_water
## 41 FALSE  220  83.0188679           wastewater
## 42  TRUE  309 116.6037736           wastewater
## 43 FALSE  526 198.4905660          septic_tank
## 44  TRUE    3   1.1320755          septic_tank
## 45     Y   63  35.6536503             drainage
## 46     P  239 135.2574986             drainage
## 47     N  227 128.4663271             drainage
## 48 FALSE  223  84.1509434                 tree
## 49  TRUE  306 115.4716981                 tree
## 50 FALSE  162  61.1320755           ground_veg
## 51  TRUE  367 138.4905660           ground_veg
## 52 FALSE  490 184.9056604        deforestation
## 53  TRUE   39  14.7169811        deforestation
## 54 FALSE  363 136.9811321               banana
## 55  TRUE  166  62.6415094               banana
## 56     A    3   2.8301887                angle
## 57     B   46  43.3962264                angle
## 58     C   82  77.3584906                angle
## 59     D  293 276.4150943                angle
## 60     E  105  99.0566038                angle
## 61     B  459 259.7623090             building
## 62     W   39  22.0713073             building
## 63     M   31  17.5438596             building
## 64    d1   83  62.6415094              density
## 65    d2  414 312.4528302              density
## 66    d3   32  24.1509434              density
## 67 FALSE  348 131.3207547                   EN
## 68  TRUE  181  68.3018868                   EN

TC_weath_rock, TC_rock_TC_geol_desf, fracture, TC_rock

Equation 1

f1 <- lrm(risk ~ building + EN + TC_saprolito + Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte + landfill + garbage + construction_deposit + crack + leaning_wall + scars + downward_floor +tilted + conc_rainfall_water + wastewater + leak + tree + ground_veg + banana , data=train.data, x=TRUE , y=TRUE)

f1 <- lrm(risk ~ building + EN + TC_saprolito + Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte + landfill + garbage + construction_deposit + crack + leaning_wall + scars + downward_floor +tilted + conc_rainfall_water + wastewater + leak + tree + ground_veg + banana + septic_tank +TC_mature_Soil , data=train.data, x=TRUE , y=TRUE) print (f1 , latex =TRUE , coefs =5) stargazer(anova(f1), type=“text”, style=“default”)

# Equation 1

eq_OLR_01 <- polr(risk~ building + TC_saprolito +
                  Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte +
                  landfill + garbage + construction_deposit + crack +
                  leaning_wall + scars + downward_floor +tilted +
                  conc_rainfall_water + wastewater + leak + tree + ground_veg + banana + septic_tank + TC_mature_Soil + deforestation, data= train.data
           ,  method = "logistic", Hess = TRUE)
ctable <- coef(summary(eq_OLR_01))



p<- pnorm(abs(ctable[, "t value"]), lower.tail = FALSE*2) #computes p value
ctable <- cbind(ctable, "p value" = p )

ctable
##                                Value Std. Error     t value      p value
## building.L                0.07094632  0.3336430  0.21264144 4.158033e-01
## building.Q               -0.91120855  0.4059388 -2.24469450 1.239388e-02
## TC_saprolitoTRUE         -0.34737837  0.3089876 -1.12424681 1.304542e-01
## TaterroTRUE              -0.20983077  0.3773479 -0.55606713 2.890825e-01
## DepEncNaturalTRUE        -0.01146158  0.3744275 -0.03061095 4.877899e-01
## DepTaludeAterroTRUE       0.52538982  0.6968580  0.75394105 2.254423e-01
## DepTaludeCorteTRUE        0.49454633  0.3120840  1.58465793 5.652204e-02
## landfillTRUE              0.16610019  0.3239652  0.51270999 3.040771e-01
## garbageTRUE               0.46351801  0.3642848  1.27240543 1.016146e-01
## construction_depositTRUE -0.32671167  0.3612172 -0.90447431 1.828720e-01
## crackTRUE                 1.81113915  0.3437891  5.26816864 6.889575e-08
## leaning_wallTRUE          1.53540429  0.5103865  3.00831697 1.313495e-03
## scarsTRUE                 4.23860691  0.4168321 10.16861926 1.368809e-24
## downward_floorTRUE        1.60422390  0.3998411  4.01215323 3.008371e-05
## tiltedTRUE                0.83857882  0.3350905  2.50254447 6.165207e-03
## conc_rainfall_waterTRUE   2.00815900  0.5384577  3.72946488 9.594342e-05
## wastewaterTRUE            0.73377024  0.2333716  3.14421399 8.326681e-04
## leakTRUE                 -0.03021594  0.2409709 -0.12539252 4.501064e-01
## treeTRUE                  0.16158956  0.2462373  0.65623504 2.558365e-01
## ground_vegTRUE            0.99736210  0.2712461  3.67696389 1.180132e-04
## bananaTRUE                0.20834658  0.2600855  0.80106954 2.115457e-01
## septic_tankTRUE          -0.10852067  1.5260101 -0.07111399 4.716535e-01
## TC_mature_SoilTRUE        0.63349693  0.2255451  2.80873695 2.486813e-03
## deforestationTRUE        -0.01750063  0.3900026 -0.04487312 4.821042e-01
## R1|R2                     1.35724196  0.5650755  2.40187718 8.155592e-03
## R2|R3                     5.32097384  0.6381140  8.33859414 3.758948e-17
## R3|R4                    10.83562282  0.7936361 13.65313808 9.668439e-43
stargazer((ctable), type="text", style="default", digits = 2)
## 
## =========================================================
##                          Value Std. Error t value p value
## ---------------------------------------------------------
## building.L               0.07     0.33     0.21    0.42  
## building.Q               -0.91    0.41     -2.24   0.01  
## TC_saprolitoTRUE         -0.35    0.31     -1.12   0.13  
## TaterroTRUE              -0.21    0.38     -0.56   0.29  
## DepEncNaturalTRUE        -0.01    0.37     -0.03   0.49  
## DepTaludeAterroTRUE      0.53     0.70     0.75    0.23  
## DepTaludeCorteTRUE       0.49     0.31     1.58    0.06  
## landfillTRUE             0.17     0.32     0.51    0.30  
## garbageTRUE              0.46     0.36     1.27    0.10  
## construction_depositTRUE -0.33    0.36     -0.90   0.18  
## crackTRUE                1.81     0.34     5.27   0.0000 
## leaning_wallTRUE         1.54     0.51     3.01    0.001 
## scarsTRUE                4.24     0.42     10.17     0   
## downward_floorTRUE       1.60     0.40     4.01   0.0000 
## tiltedTRUE               0.84     0.34     2.50    0.01  
## conc_rainfall_waterTRUE  2.01     0.54     3.73   0.0001 
## wastewaterTRUE           0.73     0.23     3.14    0.001 
## leakTRUE                 -0.03    0.24     -0.13   0.45  
## treeTRUE                 0.16     0.25     0.66    0.26  
## ground_vegTRUE           1.00     0.27     3.68   0.0001 
## bananaTRUE               0.21     0.26     0.80    0.21  
## septic_tankTRUE          -0.11    1.53     -0.07   0.47  
## TC_mature_SoilTRUE       0.63     0.23     2.81    0.002 
## deforestationTRUE        -0.02    0.39     -0.04   0.48  
## R1| R2                   1.36     0.57     2.40    0.01  
## R2| R3                   5.32     0.64     8.34      0   
## R3| R4                   10.84    0.79     13.65     0   
## ---------------------------------------------------------

less p-value = 0.10 (TC_saprolitoTRUE,TaterroTRUE, DepTaludeAterroTRUE,DepTaludeAterroTRUE,landfillTRUE, construction_depositTRUE, leakTRUE)

par(mfrow=c(6,4))
plot.xmean.ordinaly (risk~ building + TC_saprolito +
                  Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte +
                  landfill + garbage + construction_deposit + crack +
                  leaning_wall + scars + downward_floor +tilted +
                  conc_rainfall_water + wastewater + leak + tree + ground_veg + banana + septic_tank + TC_mature_Soil + deforestation
          ,data=train.data, cr=TRUE , subn=FALSE ,  cex.lab=1.5, cex.axis=2, cex.sub=2, cex.main=2)

Creating function with four level

Equation 1

sf <- function (y) {
        c('y>=1' = qlogis(mean(y>=1)),
          'y>=2' = qlogis(mean(y>=2)),
           'y>=3' = qlogis(mean(y>=3)),
            'y>=4' = qlogis(mean(y>=4)))
}

s<-with(train.data, summary(as.numeric(risk)~building + TC_saprolito +
                  Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte +
                  landfill + garbage + construction_deposit + crack +
                  leaning_wall + scars + downward_floor +tilted +
                  conc_rainfall_water + wastewater + leak + tree + ground_veg + banana + septic_tank + TC_mature_Soil + deforestation
, fun=sf))
s
## as.numeric(risk)     N= 529 
## 
## +--------------------+---+---+----+----------+-----------+-----------+
## |                    |   |N  |y>=1|y>=2      |y>=3       |y>=4       |
## +--------------------+---+---+----+----------+-----------+-----------+
## |building            |B  |459|Inf | 1.9139271|-0.22314355|-2.49438539|
## |                    |W  | 39|Inf | 2.4849066| 1.51982575|-0.05129329|
## |                    |M  | 31|Inf | 2.2335922| 1.05605267|-0.89381788|
## +--------------------+---+---+----+----------+-----------+-----------+
## |TC_saprolito        |No |451|Inf | 1.8937244|-0.11097851|-2.05963891|
## |                    |Yes| 78|Inf | 2.4849066| 0.36290549|-1.70474809|
## +--------------------+---+---+----+----------+-----------+-----------+
## |Taterro             |No |469|Inf | 1.8632184|-0.12382535|-2.10365580|
## |                    |Yes| 60|Inf | 3.3672958| 0.61903921|-1.38629436|
## +--------------------+---+---+----+----------+-----------+-----------+
## |DepEncNatural       |No |395|Inf | 1.7002671|-0.46918092|-2.46316666|
## |                    |Yes|134|Inf | 3.4812401| 1.37699197|-1.15923691|
## +--------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeAterro     |No |510|Inf | 1.9236870|-0.10204925|-2.11296423|
## |                    |Yes| 19|Inf |       Inf| 2.14006616|-0.31845373|
## +--------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeCorte      |No |310|Inf | 1.5561934|-0.39204209|-2.47793798|
## |                    |Yes|219|Inf | 2.9396428| 0.45518854|-1.52939520|
## +--------------------+---+---+----+----------+-----------+-----------+
## |landfill            |No |331|Inf | 1.5490288|-0.57746278|-2.74406064|
## |                    |Yes|198|Inf | 3.3063633| 0.88119941|-1.28222500|
## +--------------------+---+---+----+----------+-----------+-----------+
## |garbage             |No |355|Inf | 1.7181262|-0.33550652|-2.53796121|
## |                    |Yes|174|Inf | 2.6958549| 0.56639547|-1.30906301|
## +--------------------+---+---+----+----------+-----------+-----------+
## |construction_deposit|No |322|Inf | 1.6244195|-0.45488999|-2.39113849|
## |                    |Yes|207|Inf | 2.7880929| 0.60738036|-1.55814462|
## +--------------------+---+---+----+----------+-----------+-----------+
## |crack               |No |444|Inf | 1.7812882|-0.40171276|-2.73724936|
## |                    |Yes| 85|Inf | 4.4308168| 3.00815479|-0.30830136|
## +--------------------+---+---+----+----------+-----------+-----------+
## |leaning_wall        |No |497|Inf | 1.8940383|-0.15726498|-2.23582188|
## |                    |Yes| 32|Inf |       Inf| 2.70805020|-0.12516314|
## +--------------------+---+---+----+----------+-----------+-----------+
## |scars               |No |322|Inf | 1.3746888|-1.55814462|-4.37575702|
## |                    |Yes|207|Inf |       Inf| 3.92691162|-0.91967483|
## +--------------------+---+---+----+----------+-----------+-----------+
## |downward_floor      |No |469|Inf | 1.8270276|-0.29639401|-2.45750768|
## |                    |Yes| 60|Inf |       Inf| 4.07753744|-0.26826399|
## +--------------------+---+---+----+----------+-----------+-----------+
## |tilted              |No |433|Inf | 1.7519136|-0.46550250|-2.59773918|
## |                    |Yes| 96|Inf | 4.5538769| 3.13549422|-0.64662716|
## +--------------------+---+---+----+----------+-----------+-----------+
## |conc_rainfall_water |No | 23|Inf |-1.0414539|       -Inf|       -Inf|
## |                    |Yes|506|Inf | 2.2556682| 0.04743973|-1.95043504|
## +--------------------+---+---+----+----------+-----------+-----------+
## |wastewater          |No |220|Inf | 1.3031440|-0.57931204|-3.04452244|
## |                    |Yes|309|Inf | 2.7829515| 0.33314445|-1.57488553|
## +--------------------+---+---+----+----------+-----------+-----------+
## |leak                |No |345|Inf | 1.6625477|-0.35737892|-2.59338729|
## |                    |Yes|184|Inf | 2.8564702| 0.55748132|-1.31317210|
## +--------------------+---+---+----+----------+-----------+-----------+
## |tree                |No |223|Inf | 1.3475083|-0.67972416|-2.37368101|
## |                    |Yes|306|Inf | 2.7150432| 0.41091471|-1.78415487|
## +--------------------+---+---+----+----------+-----------+-----------+
## |ground_veg          |No |162|Inf | 0.9249488|-1.36330484|-2.95751106|
## |                    |Yes|367|Inf | 2.9077635| 0.47177511|-1.73567000|
## +--------------------+---+---+----+----------+-----------+-----------+
## |banana              |No |363|Inf | 1.5995532|-0.40776132|-2.23766555|
## |                    |Yes|166|Inf | 3.7013020| 0.78495473|-1.59504917|
## +--------------------+---+---+----+----------+-----------+-----------+
## |septic_tank         |No |526|Inf | 1.9590108|-0.04563529|-2.01275017|
## |                    |Yes|  3|Inf |       Inf| 0.69314718|-0.69314718|
## +--------------------+---+---+----+----------+-----------+-----------+
## |TC_mature_Soil      |No |274|Inf | 1.5493340|-0.32397207|-2.21355147|
## |                    |Yes|255|Inf | 2.6390573| 0.26028310|-1.80555279|
## +--------------------+---+---+----+----------+-----------+-----------+
## |deforestation       |No |490|Inf | 2.0276865| 0.04082199|-1.96944065|
## |                    |Yes| 39|Inf | 1.3545457|-1.20397280|-2.48490665|
## +--------------------+---+---+----+----------+-----------+-----------+
## |Overall             |   |529|Inf | 1.9654973|-0.04159390|-2.00105091|
## +--------------------+---+---+----+----------+-----------+-----------+
plot(s, which=1:4, pch=1:4, xlab='logit', main=' ', xlim=c(-5,5), cex.lab=1.5, cex.axis=1.5, cex.sub=1.5)

Equation 2

  • parameters okay and so/so
  • porportion
  • excluded TC_geol_desf

f2 <- lrm(risk ~ angle + building + EN + TC_saprolito + Taterro + DepEncNatural + DepTaludeAterro + DepTaludeCorte + landfill + garbage + construction_deposit + crack + leaning_wall + scars + downward_floor +tilted + conc_rainfall_water + wastewater + leak + drainage + TC_mature_Soil + density + TC + tree +ground_veg + deforestation + banana , data=train.data, x=TRUE , y=TRUE)

      stargazer(anova(f2), type="text", style="default")
eq_OLR_02 <- polr(risk ~ angle +building + EN + TC_saprolito+ Taterro+ TC_mature_Soil+ DepEncNatural+ DepTaludeAterro+  DepTaludeCorte+ landfill+garbage+ construction_deposit+ leak+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ conc_rainfall_water+ wastewater+ tree+ ground_veg+ banana+ deforestation + density+ TC,
                  
                 data= train.data
           ,  method = "logistic", Hess = TRUE)
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
ctable <- coef(summary(eq_OLR_02))








p<- pnorm(abs(ctable[, "t value"]), lower.tail = FALSE*2) #computes p value
ctable <- cbind(ctable, "p value" = p )

ctable
##                                Value Std. Error     t value      p value
## angleB                   -0.84788186  1.6826178 -0.50390639 3.071636e-01
## angleC                    0.33075167  1.6672048  0.19838694 4.213712e-01
## angleD                    0.86623957  1.6643160  0.52047783 3.013653e-01
## angleE                    1.73154332  1.6772507  1.03237002 1.509494e-01
## building.L                0.08863771  0.3292826  0.26918434 3.938939e-01
## building.Q               -1.14876125  0.4237232 -2.71111271 3.352891e-03
## ENTRUE                    0.86790687  0.3818389  2.27296610 1.151411e-02
## TC_saprolitoTRUE         -0.55909302  0.3259522 -1.71526087 4.314870e-02
## TaterroTRUE              -0.14779141  0.3931371 -0.37592846 3.534850e-01
## TC_mature_SoilTRUE        0.44558998  0.2384024  1.86906663 3.080677e-02
## DepEncNaturalTRUE        -0.65256017  0.4754871 -1.37240357 8.496892e-02
## DepTaludeAterroTRUE       0.92682842  0.7122352  1.30129546 9.657867e-02
## DepTaludeCorteTRUE        0.36686195  0.3338527  1.09887382 1.359116e-01
## landfillTRUE              0.34253753  0.3289970  1.04115706 1.489013e-01
## garbageTRUE               0.49227005  0.3793141  1.29778996 9.717976e-02
## construction_depositTRUE -0.23156955  0.3737954 -0.61950888 2.677906e-01
## leakTRUE                 -0.01132889  0.2499427 -0.04532597 4.819237e-01
## crackTRUE                 1.79585420  0.3584548  5.00998773 2.721675e-07
## leaning_wallTRUE          1.35756400  0.4979579  2.72626265 3.202800e-03
## scarsTRUE                 4.45479463  0.4303899 10.35060184 2.079317e-25
## downward_floorTRUE        1.62646688  0.4146012  3.92296710 4.373255e-05
## tiltedTRUE                0.80347723  0.3376836  2.37937917 8.670914e-03
## conc_rainfall_waterTRUE   1.63639207  0.6179825  2.64795841 4.048974e-03
## wastewaterTRUE            0.87212399  0.2477209  3.52059051 2.152935e-04
## treeTRUE                  0.01201290  0.2550986  0.04709120 4.812203e-01
## ground_vegTRUE            0.67437265  0.2813377  2.39702215 8.264462e-03
## bananaTRUE                0.02952891  0.2710396  0.10894687 4.566223e-01
## deforestationTRUE        -0.32509304  0.4042441 -0.80419992 2.106408e-01
## densityd2                 0.28415914  0.3209598  0.88534191 1.879861e-01
## densityd3                 0.13237882  0.5858140  0.22597414 4.106108e-01
## TCTRUE                    0.85025534  0.4641643  1.83179816 3.349075e-02
## R1|R2                     2.23358030  1.7627521  1.26709837 1.025601e-01
## R2|R3                     6.61028550  1.7978169  3.67684023 1.180704e-04
## R3|R4                    12.39604142  1.8824340  6.58511354 2.272690e-11
stargazer((ctable), type="text", style="default", digits=2)
## 
## =========================================================
##                          Value Std. Error t value p value
## ---------------------------------------------------------
## angleB                   -0.85    1.68     -0.50   0.31  
## angleC                   0.33     1.67     0.20    0.42  
## angleD                   0.87     1.66     0.52    0.30  
## angleE                   1.73     1.68     1.03    0.15  
## building.L               0.09     0.33     0.27    0.39  
## building.Q               -1.15    0.42     -2.71   0.003 
## ENTRUE                   0.87     0.38     2.27    0.01  
## TC_saprolitoTRUE         -0.56    0.33     -1.72   0.04  
## TaterroTRUE              -0.15    0.39     -0.38   0.35  
## TC_mature_SoilTRUE       0.45     0.24     1.87    0.03  
## DepEncNaturalTRUE        -0.65    0.48     -1.37   0.08  
## DepTaludeAterroTRUE      0.93     0.71     1.30    0.10  
## DepTaludeCorteTRUE       0.37     0.33     1.10    0.14  
## landfillTRUE             0.34     0.33     1.04    0.15  
## garbageTRUE              0.49     0.38     1.30    0.10  
## construction_depositTRUE -0.23    0.37     -0.62   0.27  
## leakTRUE                 -0.01    0.25     -0.05   0.48  
## crackTRUE                1.80     0.36     5.01   0.0000 
## leaning_wallTRUE         1.36     0.50     2.73    0.003 
## scarsTRUE                4.45     0.43     10.35     0   
## downward_floorTRUE       1.63     0.41     3.92   0.0000 
## tiltedTRUE               0.80     0.34     2.38    0.01  
## conc_rainfall_waterTRUE  1.64     0.62     2.65    0.004 
## wastewaterTRUE           0.87     0.25     3.52   0.0002 
## treeTRUE                 0.01     0.26     0.05    0.48  
## ground_vegTRUE           0.67     0.28     2.40    0.01  
## bananaTRUE               0.03     0.27     0.11    0.46  
## deforestationTRUE        -0.33    0.40     -0.80   0.21  
## densityd2                0.28     0.32     0.89    0.19  
## densityd3                0.13     0.59     0.23    0.41  
## TCTRUE                   0.85     0.46     1.83    0.03  
## R1| R2                   2.23     1.76     1.27    0.10  
## R2| R3                   6.61     1.80     3.68   0.0001 
## R3| R4                   12.40    1.88     6.59      0   
## ---------------------------------------------------------
par(mfrow=c(7,4))
plot.xmean.ordinaly (risk~ angle +building + EN + TC_saprolito+ Taterro+ TC_mature_Soil+ DepEncNatural+ DepTaludeAterro+  DepTaludeCorte+ landfill+garbage+ construction_deposit+ leak+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ conc_rainfall_water+ wastewater+ tree+ ground_veg+ banana+ deforestation + density+ TC
          ,data=train.data, cr=TRUE , subn=FALSE ,  cex.lab=1.5, cex.axis=4, cex.sub=4, cex.main=4)

sf <- function (y) {
        c('y>=1' = qlogis(mean(y>=1)),
          'y>=2' = qlogis(mean(y>=2)),
           'y>=3' = qlogis(mean(y>=3)),
            'y>=4' = qlogis(mean(y>=4)))
}

s<-with(train.data, summary(as.numeric(risk)~angle +building + EN + TC_saprolito+ Taterro+ TC_mature_Soil+ DepEncNatural+ DepTaludeAterro+  DepTaludeCorte+ landfill+garbage+ construction_deposit+ leak+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ conc_rainfall_water+ wastewater+ tree+ ground_veg+ banana+ deforestation + density+ TC,data=train.data
, fun=sf))
s
## as.numeric(risk)     N= 529 
## 
## +--------------------+---+---+----+----------+-----------+-----------+
## |                    |   |N  |y>=1|y>=2      |y>=3       |y>=4       |
## +--------------------+---+---+----+----------+-----------+-----------+
## |angle               |A  |  3|Inf | 0.6931472|       -Inf|       -Inf|
## |                    |B  | 46|Inf |-0.3513979|-1.89711998|-3.80666249|
## |                    |C  | 82|Inf | 1.6691571|-1.00330211|-3.27083556|
## |                    |D  |293|Inf | 2.6137395| 0.33764251|-1.84451003|
## |                    |E  |105|Inf | 3.2288262| 0.28768207|-1.50990832|
## +--------------------+---+---+----+----------+-----------+-----------+
## |building            |B  |459|Inf | 1.9139271|-0.22314355|-2.49438539|
## |                    |W  | 39|Inf | 2.4849066| 1.51982575|-0.05129329|
## |                    |M  | 31|Inf | 2.2335922| 1.05605267|-0.89381788|
## +--------------------+---+---+----+----------+-----------+-----------+
## |EN                  |No |348|Inf | 1.5288574|-0.50470003|-2.51645501|
## |                    |Yes|181|Inf | 4.0831713| 0.88173835|-1.35889539|
## +--------------------+---+---+----+----------+-----------+-----------+
## |TC_saprolito        |No |451|Inf | 1.8937244|-0.11097851|-2.05963891|
## |                    |Yes| 78|Inf | 2.4849066| 0.36290549|-1.70474809|
## +--------------------+---+---+----+----------+-----------+-----------+
## |Taterro             |No |469|Inf | 1.8632184|-0.12382535|-2.10365580|
## |                    |Yes| 60|Inf | 3.3672958| 0.61903921|-1.38629436|
## +--------------------+---+---+----+----------+-----------+-----------+
## |TC_mature_Soil      |No |274|Inf | 1.5493340|-0.32397207|-2.21355147|
## |                    |Yes|255|Inf | 2.6390573| 0.26028310|-1.80555279|
## +--------------------+---+---+----+----------+-----------+-----------+
## |DepEncNatural       |No |395|Inf | 1.7002671|-0.46918092|-2.46316666|
## |                    |Yes|134|Inf | 3.4812401| 1.37699197|-1.15923691|
## +--------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeAterro     |No |510|Inf | 1.9236870|-0.10204925|-2.11296423|
## |                    |Yes| 19|Inf |       Inf| 2.14006616|-0.31845373|
## +--------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeCorte      |No |310|Inf | 1.5561934|-0.39204209|-2.47793798|
## |                    |Yes|219|Inf | 2.9396428| 0.45518854|-1.52939520|
## +--------------------+---+---+----+----------+-----------+-----------+
## |landfill            |No |331|Inf | 1.5490288|-0.57746278|-2.74406064|
## |                    |Yes|198|Inf | 3.3063633| 0.88119941|-1.28222500|
## +--------------------+---+---+----+----------+-----------+-----------+
## |garbage             |No |355|Inf | 1.7181262|-0.33550652|-2.53796121|
## |                    |Yes|174|Inf | 2.6958549| 0.56639547|-1.30906301|
## +--------------------+---+---+----+----------+-----------+-----------+
## |construction_deposit|No |322|Inf | 1.6244195|-0.45488999|-2.39113849|
## |                    |Yes|207|Inf | 2.7880929| 0.60738036|-1.55814462|
## +--------------------+---+---+----+----------+-----------+-----------+
## |leak                |No |345|Inf | 1.6625477|-0.35737892|-2.59338729|
## |                    |Yes|184|Inf | 2.8564702| 0.55748132|-1.31317210|
## +--------------------+---+---+----+----------+-----------+-----------+
## |crack               |No |444|Inf | 1.7812882|-0.40171276|-2.73724936|
## |                    |Yes| 85|Inf | 4.4308168| 3.00815479|-0.30830136|
## +--------------------+---+---+----+----------+-----------+-----------+
## |leaning_wall        |No |497|Inf | 1.8940383|-0.15726498|-2.23582188|
## |                    |Yes| 32|Inf |       Inf| 2.70805020|-0.12516314|
## +--------------------+---+---+----+----------+-----------+-----------+
## |scars               |No |322|Inf | 1.3746888|-1.55814462|-4.37575702|
## |                    |Yes|207|Inf |       Inf| 3.92691162|-0.91967483|
## +--------------------+---+---+----+----------+-----------+-----------+
## |downward_floor      |No |469|Inf | 1.8270276|-0.29639401|-2.45750768|
## |                    |Yes| 60|Inf |       Inf| 4.07753744|-0.26826399|
## +--------------------+---+---+----+----------+-----------+-----------+
## |tilted              |No |433|Inf | 1.7519136|-0.46550250|-2.59773918|
## |                    |Yes| 96|Inf | 4.5538769| 3.13549422|-0.64662716|
## +--------------------+---+---+----+----------+-----------+-----------+
## |conc_rainfall_water |No | 23|Inf |-1.0414539|       -Inf|       -Inf|
## |                    |Yes|506|Inf | 2.2556682| 0.04743973|-1.95043504|
## +--------------------+---+---+----+----------+-----------+-----------+
## |wastewater          |No |220|Inf | 1.3031440|-0.57931204|-3.04452244|
## |                    |Yes|309|Inf | 2.7829515| 0.33314445|-1.57488553|
## +--------------------+---+---+----+----------+-----------+-----------+
## |tree                |No |223|Inf | 1.3475083|-0.67972416|-2.37368101|
## |                    |Yes|306|Inf | 2.7150432| 0.41091471|-1.78415487|
## +--------------------+---+---+----+----------+-----------+-----------+
## |ground_veg          |No |162|Inf | 0.9249488|-1.36330484|-2.95751106|
## |                    |Yes|367|Inf | 2.9077635| 0.47177511|-1.73567000|
## +--------------------+---+---+----+----------+-----------+-----------+
## |banana              |No |363|Inf | 1.5995532|-0.40776132|-2.23766555|
## |                    |Yes|166|Inf | 3.7013020| 0.78495473|-1.59504917|
## +--------------------+---+---+----+----------+-----------+-----------+
## |deforestation       |No |490|Inf | 2.0276865| 0.04082199|-1.96944065|
## |                    |Yes| 39|Inf | 1.3545457|-1.20397280|-2.48490665|
## +--------------------+---+---+----+----------+-----------+-----------+
## |density             |d1 | 83|Inf | 0.8415672|-1.28401551|-3.28341435|
## |                    |d2 |414|Inf | 2.2633644| 0.05798726|-2.03143232|
## |                    |d3 | 32|Inf | 3.4339872| 1.94591015|-0.51082562|
## +--------------------+---+---+----+----------+-----------+-----------+
## |TC                  |No | 46|Inf | 0.6286087|-0.17435339|-1.41369334|
## |                    |Yes|483|Inf | 2.1812242|-0.02898754|-2.07247287|
## +--------------------+---+---+----+----------+-----------+-----------+
## |Overall             |   |529|Inf | 1.9654973|-0.04159390|-2.00105091|
## +--------------------+---+---+----+----------+-----------+-----------+
plot(s, which=1:4, pch=1:4, xlab='logit', main=' ', xlim=c(-5,5), cex.lab=1, cex.axis=2, cex.sub=1)

Equation 3

  • parameters okay and so/so
  • porportion
  • p-value based equation 2 > 0.5

f3 <- lrm(risk ~ angle +building + EN + DepTaludeAterro+ DepTaludeCorte+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ conc_rainfall_water+ wastewater+ tree + TC , data=train.data, x=TRUE , y=TRUE) stargazer(anova(f3), type=“text”, style=“default”)

# x=TRUE, y=TRUE used by resid() below 

eq_OLR_03 <- polr(risk ~ building + EN + DepTaludeAterro+  DepTaludeCorte+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ground_veg + conc_rainfall_water+tree+ wastewater + TC,
 data= train.data
           ,  method = "logistic", Hess = TRUE)
ctable <- coef(summary(eq_OLR_03))


p<- pnorm(abs(ctable[, "t value"]), lower.tail = FALSE*2) #computes p value
ctable <- cbind(ctable, "p value" = p )

ctable
##                               Value Std. Error    t value      p value
## building.L               0.26241262  0.3150563  0.8329070 2.024486e-01
## building.Q              -0.72388871  0.3855956 -1.8773261 3.023671e-02
## ENTRUE                   0.66638667  0.2615206  2.5481227 5.415218e-03
## DepTaludeAterroTRUE      0.84046001  0.6138799  1.3690952 8.548476e-02
## DepTaludeCorteTRUE       0.73204989  0.2325230  3.1482900 8.211434e-04
## crackTRUE                1.82548294  0.3367049  5.4216115 2.953207e-08
## leaning_wallTRUE         1.53503787  0.5057375  3.0352463 1.201696e-03
## scarsTRUE                4.15984030  0.4123002 10.0893489 3.078829e-24
## downward_floorTRUE       1.77891498  0.3831399  4.6429901 1.717014e-06
## tiltedTRUE               0.75098944  0.3222342  2.3305702 9.888017e-03
## ground_vegTRUE           0.87709262  0.2642600  3.3190523 4.516176e-04
## conc_rainfall_waterTRUE  1.98289853  0.5356525  3.7018373 1.070219e-04
## treeTRUE                 0.06340334  0.2357134  0.2689849 3.939706e-01
## wastewaterTRUE           0.76213640  0.2242307  3.3988947 3.382938e-04
## TCTRUE                   1.09953216  0.4125784  2.6650257 3.849122e-03
## R1|R2                    2.11354366  0.6612664  3.1962061 6.962381e-04
## R2|R3                    6.05886768  0.7347163  8.2465403 8.152307e-17
## R3|R4                   11.62615237  0.8970678 12.9601717 1.028932e-38
stargazer((ctable), type="text", style="default", digits = 2)
## 
## ========================================================
##                         Value Std. Error t value p value
## --------------------------------------------------------
## building.L              0.26     0.32     0.83    0.20  
## building.Q              -0.72    0.39     -1.88   0.03  
## ENTRUE                  0.67     0.26     2.55    0.01  
## DepTaludeAterroTRUE     0.84     0.61     1.37    0.09  
## DepTaludeCorteTRUE      0.73     0.23     3.15    0.001 
## crackTRUE               1.83     0.34     5.42   0.0000 
## leaning_wallTRUE        1.54     0.51     3.04    0.001 
## scarsTRUE               4.16     0.41     10.09     0   
## downward_floorTRUE      1.78     0.38     4.64   0.0000 
## tiltedTRUE              0.75     0.32     2.33    0.01  
## ground_vegTRUE          0.88     0.26     3.32   0.0005 
## conc_rainfall_waterTRUE 1.98     0.54     3.70   0.0001 
## treeTRUE                0.06     0.24     0.27    0.39  
## wastewaterTRUE          0.76     0.22     3.40   0.0003 
## TCTRUE                  1.10     0.41     2.67    0.004 
## R1| R2                  2.11     0.66     3.20    0.001 
## R2| R3                  6.06     0.73     8.25      0   
## R3| R4                  11.63    0.90     12.96     0   
## --------------------------------------------------------
#print (f3 , latex =TRUE , coefs =5)
par(mfrow=c(3,5))
plot.xmean.ordinaly (risk ~  building + EN + DepTaludeAterro+  DepTaludeCorte+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ground_veg + conc_rainfall_water+tree+ wastewater + TC,
          data=train.data, cr=TRUE , subn=FALSE , cex.points =0.65)

sf <- function (y) {
        c('y>=1' = qlogis(mean(y>=1)),
          'y>=2' = qlogis(mean(y>=2)),
           'y>=3' = qlogis(mean(y>=3)),
            'y>=4' = qlogis(mean(y>=4)))
}

s<-with(train.data, summary(as.numeric(risk)~building + EN + DepTaludeAterro+  DepTaludeCorte+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ground_veg + conc_rainfall_water+tree+ wastewater + TC, fun=sf))
s
## as.numeric(risk)     N= 529 
## 
## +-------------------+---+---+----+----------+-----------+-----------+
## |                   |   |N  |y>=1|y>=2      |y>=3       |y>=4       |
## +-------------------+---+---+----+----------+-----------+-----------+
## |building           |B  |459|Inf | 1.9139271|-0.22314355|-2.49438539|
## |                   |W  | 39|Inf | 2.4849066| 1.51982575|-0.05129329|
## |                   |M  | 31|Inf | 2.2335922| 1.05605267|-0.89381788|
## +-------------------+---+---+----+----------+-----------+-----------+
## |EN                 |No |348|Inf | 1.5288574|-0.50470003|-2.51645501|
## |                   |Yes|181|Inf | 4.0831713| 0.88173835|-1.35889539|
## +-------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeAterro    |No |510|Inf | 1.9236870|-0.10204925|-2.11296423|
## |                   |Yes| 19|Inf |       Inf| 2.14006616|-0.31845373|
## +-------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeCorte     |No |310|Inf | 1.5561934|-0.39204209|-2.47793798|
## |                   |Yes|219|Inf | 2.9396428| 0.45518854|-1.52939520|
## +-------------------+---+---+----+----------+-----------+-----------+
## |crack              |No |444|Inf | 1.7812882|-0.40171276|-2.73724936|
## |                   |Yes| 85|Inf | 4.4308168| 3.00815479|-0.30830136|
## +-------------------+---+---+----+----------+-----------+-----------+
## |leaning_wall       |No |497|Inf | 1.8940383|-0.15726498|-2.23582188|
## |                   |Yes| 32|Inf |       Inf| 2.70805020|-0.12516314|
## +-------------------+---+---+----+----------+-----------+-----------+
## |scars              |No |322|Inf | 1.3746888|-1.55814462|-4.37575702|
## |                   |Yes|207|Inf |       Inf| 3.92691162|-0.91967483|
## +-------------------+---+---+----+----------+-----------+-----------+
## |downward_floor     |No |469|Inf | 1.8270276|-0.29639401|-2.45750768|
## |                   |Yes| 60|Inf |       Inf| 4.07753744|-0.26826399|
## +-------------------+---+---+----+----------+-----------+-----------+
## |tilted             |No |433|Inf | 1.7519136|-0.46550250|-2.59773918|
## |                   |Yes| 96|Inf | 4.5538769| 3.13549422|-0.64662716|
## +-------------------+---+---+----+----------+-----------+-----------+
## |ground_veg         |No |162|Inf | 0.9249488|-1.36330484|-2.95751106|
## |                   |Yes|367|Inf | 2.9077635| 0.47177511|-1.73567000|
## +-------------------+---+---+----+----------+-----------+-----------+
## |conc_rainfall_water|No | 23|Inf |-1.0414539|       -Inf|       -Inf|
## |                   |Yes|506|Inf | 2.2556682| 0.04743973|-1.95043504|
## +-------------------+---+---+----+----------+-----------+-----------+
## |tree               |No |223|Inf | 1.3475083|-0.67972416|-2.37368101|
## |                   |Yes|306|Inf | 2.7150432| 0.41091471|-1.78415487|
## +-------------------+---+---+----+----------+-----------+-----------+
## |wastewater         |No |220|Inf | 1.3031440|-0.57931204|-3.04452244|
## |                   |Yes|309|Inf | 2.7829515| 0.33314445|-1.57488553|
## +-------------------+---+---+----+----------+-----------+-----------+
## |TC                 |No | 46|Inf | 0.6286087|-0.17435339|-1.41369334|
## |                   |Yes|483|Inf | 2.1812242|-0.02898754|-2.07247287|
## +-------------------+---+---+----+----------+-----------+-----------+
## |Overall            |   |529|Inf | 1.9654973|-0.04159390|-2.00105091|
## +-------------------+---+---+----+----------+-----------+-----------+
plot(s, which=1:4, pch=1:4, xlab='logit', main=' ', xlim=c(-5,5), cex.lab=0.6, cex.axis=0.6, cex.sub=0.6)

Equation 4

  • p-value equation 3 > 0.05 (banana, DepTaludeCorte)
  • consider proportion
  • paremeters okay & so/so
  • fashion order

f4 <- lrm(risk ~ building + EN
+ DepEncNatural
+ crack + leaning_wall + scars + downward_floor +tilted + conc_rainfall_water + wastewater + drainage + TC_mature_Soil + TC + +ground_veg
,data=train.data, x=TRUE , y=TRUE) # x=TRUE, y=TRUE used by resid() below #print (f4 , latex =TRUE , coefs =5) stargazer(anova(f4), type=“text”, style=“default”)

eq_OLR_04 <- polr(risk~  building + EN + DepTaludeAterro+  DepTaludeCorte+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ground_veg + conc_rainfall_water+ wastewater + TC
                  , data= train.data
           ,  method = "logistic", Hess = TRUE)
p<- pnorm(abs(ctable[, "t value"]), lower.tail = FALSE*2) #computes p value

ctable <- coef(summary(eq_OLR_04))

ctable <- cbind(ctable, "p value" = p )
## Warning in cbind(ctable, `p value` = p): number of rows of result is not a
## multiple of vector length (arg 2)
ctable
##                              Value Std. Error    t value      p value
## building.L               0.2629616  0.3149305  0.8349832 2.024486e-01
## building.Q              -0.7161186  0.3841402 -1.8642117 3.023671e-02
## ENTRUE                   0.6800541  0.2565437  2.6508314 5.415218e-03
## DepTaludeAterroTRUE      0.8446356  0.6141265  1.3753447 8.548476e-02
## DepTaludeCorteTRUE       0.7351022  0.2321836  3.1660390 8.211434e-04
## crackTRUE                1.8188662  0.3357861  5.4167409 2.953207e-08
## leaning_wallTRUE         1.5460019  0.5035353  3.0702953 1.201696e-03
## scarsTRUE                4.1664899  0.4115675 10.1234675 3.078829e-24
## downward_floorTRUE       1.7826202  0.3829802  4.6546014 1.717014e-06
## tiltedTRUE               0.7491251  0.3220702  2.3259686 9.888017e-03
## ground_vegTRUE           0.8997904  0.2504026  3.5933747 4.516176e-04
## conc_rainfall_waterTRUE  1.9855042  0.5356878  3.7064580 1.070219e-04
## wastewaterTRUE           0.7583775  0.2238244  3.3882696 3.939706e-01
## TCTRUE                   1.1092735  0.4109917  2.6990168 3.382938e-04
## R1|R2                    2.1133904  0.6612173  3.1962118 3.849122e-03
## R2|R3                    6.0567924  0.7345492  8.2455914 6.962381e-04
## R3|R4                   11.6267367  0.8971842 12.9591417 8.152307e-17
stargazer((ctable), type="text", style="default", digits=2)
## 
## ========================================================
##                         Value Std. Error t value p value
## --------------------------------------------------------
## building.L              0.26     0.31     0.83    0.20  
## building.Q              -0.72    0.38     -1.86   0.03  
## ENTRUE                  0.68     0.26     2.65    0.01  
## DepTaludeAterroTRUE     0.84     0.61     1.38    0.09  
## DepTaludeCorteTRUE      0.74     0.23     3.17    0.001 
## crackTRUE               1.82     0.34     5.42   0.0000 
## leaning_wallTRUE        1.55     0.50     3.07    0.001 
## scarsTRUE               4.17     0.41     10.12     0   
## downward_floorTRUE      1.78     0.38     4.65   0.0000 
## tiltedTRUE              0.75     0.32     2.33    0.01  
## ground_vegTRUE          0.90     0.25     3.59   0.0005 
## conc_rainfall_waterTRUE 1.99     0.54     3.71   0.0001 
## wastewaterTRUE          0.76     0.22     3.39    0.39  
## TCTRUE                  1.11     0.41     2.70   0.0003 
## R1| R2                  2.11     0.66     3.20    0.004 
## R2| R3                  6.06     0.73     8.25    0.001 
## R3| R4                  11.63    0.90     12.96     0   
## --------------------------------------------------------
par(mfrow=c(4,4))
plot.xmean.ordinaly (risk ~  building + EN + DepTaludeAterro+  DepTaludeCorte+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ground_veg + conc_rainfall_water+ wastewater + TC
          ,data=train.data, cr=TRUE , subn=FALSE , cex.points =0.65)

sf <- function (y) {
        c('y>=1' = qlogis(mean(y>=1)),
          'y>=2' = qlogis(mean(y>=2)),
           'y>=3' = qlogis(mean(y>=3)),
            'y>=4' = qlogis(mean(y>=4)))
}

s<-with(train.data, summary(as.numeric(risk)~building + EN + DepTaludeAterro+  DepTaludeCorte+ crack+ leaning_wall+ scars+ downward_floor+ tilted+ground_veg + conc_rainfall_water+ wastewater + TC
, fun=sf))
s
## as.numeric(risk)     N= 529 
## 
## +-------------------+---+---+----+----------+-----------+-----------+
## |                   |   |N  |y>=1|y>=2      |y>=3       |y>=4       |
## +-------------------+---+---+----+----------+-----------+-----------+
## |building           |B  |459|Inf | 1.9139271|-0.22314355|-2.49438539|
## |                   |W  | 39|Inf | 2.4849066| 1.51982575|-0.05129329|
## |                   |M  | 31|Inf | 2.2335922| 1.05605267|-0.89381788|
## +-------------------+---+---+----+----------+-----------+-----------+
## |EN                 |No |348|Inf | 1.5288574|-0.50470003|-2.51645501|
## |                   |Yes|181|Inf | 4.0831713| 0.88173835|-1.35889539|
## +-------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeAterro    |No |510|Inf | 1.9236870|-0.10204925|-2.11296423|
## |                   |Yes| 19|Inf |       Inf| 2.14006616|-0.31845373|
## +-------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeCorte     |No |310|Inf | 1.5561934|-0.39204209|-2.47793798|
## |                   |Yes|219|Inf | 2.9396428| 0.45518854|-1.52939520|
## +-------------------+---+---+----+----------+-----------+-----------+
## |crack              |No |444|Inf | 1.7812882|-0.40171276|-2.73724936|
## |                   |Yes| 85|Inf | 4.4308168| 3.00815479|-0.30830136|
## +-------------------+---+---+----+----------+-----------+-----------+
## |leaning_wall       |No |497|Inf | 1.8940383|-0.15726498|-2.23582188|
## |                   |Yes| 32|Inf |       Inf| 2.70805020|-0.12516314|
## +-------------------+---+---+----+----------+-----------+-----------+
## |scars              |No |322|Inf | 1.3746888|-1.55814462|-4.37575702|
## |                   |Yes|207|Inf |       Inf| 3.92691162|-0.91967483|
## +-------------------+---+---+----+----------+-----------+-----------+
## |downward_floor     |No |469|Inf | 1.8270276|-0.29639401|-2.45750768|
## |                   |Yes| 60|Inf |       Inf| 4.07753744|-0.26826399|
## +-------------------+---+---+----+----------+-----------+-----------+
## |tilted             |No |433|Inf | 1.7519136|-0.46550250|-2.59773918|
## |                   |Yes| 96|Inf | 4.5538769| 3.13549422|-0.64662716|
## +-------------------+---+---+----+----------+-----------+-----------+
## |ground_veg         |No |162|Inf | 0.9249488|-1.36330484|-2.95751106|
## |                   |Yes|367|Inf | 2.9077635| 0.47177511|-1.73567000|
## +-------------------+---+---+----+----------+-----------+-----------+
## |conc_rainfall_water|No | 23|Inf |-1.0414539|       -Inf|       -Inf|
## |                   |Yes|506|Inf | 2.2556682| 0.04743973|-1.95043504|
## +-------------------+---+---+----+----------+-----------+-----------+
## |wastewater         |No |220|Inf | 1.3031440|-0.57931204|-3.04452244|
## |                   |Yes|309|Inf | 2.7829515| 0.33314445|-1.57488553|
## +-------------------+---+---+----+----------+-----------+-----------+
## |TC                 |No | 46|Inf | 0.6286087|-0.17435339|-1.41369334|
## |                   |Yes|483|Inf | 2.1812242|-0.02898754|-2.07247287|
## +-------------------+---+---+----+----------+-----------+-----------+
## |Overall            |   |529|Inf | 1.9654973|-0.04159390|-2.00105091|
## +-------------------+---+---+----+----------+-----------+-----------+
plot(s, which=1:4, pch=1:4, xlab='logit', main=' ', xlim=c(-5,5), cex.lab=0.7, cex.axis=0.5, cex.sub=0.5)

Equation 5 - Based on Equation 1

  • based on Eq 1
  • less p-value > 0.10 (
# x=TRUE, y=TRUE used by resid() below 
#print (f1 , latex =TRUE , coefs =5)
#stargazer(anova(f1), type="text", style="default")

eq_OLR_05 <- polr(risk ~ building+ TC_mature_Soil+ DepTaludeAterro+  DepTaludeCorte+  construction_deposit+  crack+ leaning_wall+ scars+ downward_floor+ tilted+ conc_rainfall_water+ wastewater+ ground_veg,  data= train.data
           ,  method = "logistic", Hess = TRUE)

ctable <- coef(summary(eq_OLR_05))

p<- pnorm(abs(ctable[, "t value"]), lower.tail = FALSE*2) #computes p value
ctable <- cbind(ctable, "p value" = p )

ctable
##                                Value Std. Error    t value      p value
## building.L                0.10723683  0.3193606  0.3357860 3.685161e-01
## building.Q               -0.91765427  0.3970004 -2.3114692 1.040348e-02
## TC_mature_SoilTRUE        0.63636504  0.2236484  2.8453811 2.217916e-03
## DepTaludeAterroTRUE       0.38783963  0.6055040  0.6405236 2.609161e-01
## DepTaludeCorteTRUE        0.59709739  0.2486494  2.4013627 8.167069e-03
## construction_depositTRUE  0.04921662  0.2545155  0.1933737 4.233331e-01
## crackTRUE                 1.82369931  0.3327584  5.4805510 2.120016e-08
## leaning_wallTRUE          1.54391550  0.5018794  3.0762680 1.048047e-03
## scarsTRUE                 4.21133212  0.4090227 10.2960852 3.669369e-25
## downward_floorTRUE        1.61190796  0.3845368  4.1918172 1.383645e-05
## tiltedTRUE                0.86053067  0.3229448  2.6646373 3.853569e-03
## conc_rainfall_waterTRUE   1.96109102  0.5308295  3.6943895 1.102079e-04
## wastewaterTRUE            0.74653858  0.2247991  3.3209140 4.486159e-04
## ground_vegTRUE            1.06545025  0.2407255  4.4259959 4.799917e-06
## R1|R2                     1.28345274  0.5544072  2.3150000 1.030647e-02
## R2|R3                     5.21305377  0.6255862  8.3330704 3.938614e-17
## R3|R4                    10.67191392  0.7783041 13.7117532 4.317295e-43
stargazer((ctable), type="text", style="default", digits = 2)
## 
## =========================================================
##                          Value Std. Error t value p value
## ---------------------------------------------------------
## building.L               0.11     0.32     0.34    0.37  
## building.Q               -0.92    0.40     -2.31   0.01  
## TC_mature_SoilTRUE       0.64     0.22     2.85    0.002 
## DepTaludeAterroTRUE      0.39     0.61     0.64    0.26  
## DepTaludeCorteTRUE       0.60     0.25     2.40    0.01  
## construction_depositTRUE 0.05     0.25     0.19    0.42  
## crackTRUE                1.82     0.33     5.48   0.0000 
## leaning_wallTRUE         1.54     0.50     3.08    0.001 
## scarsTRUE                4.21     0.41     10.30     0   
## downward_floorTRUE       1.61     0.38     4.19   0.0000 
## tiltedTRUE               0.86     0.32     2.66    0.004 
## conc_rainfall_waterTRUE  1.96     0.53     3.69   0.0001 
## wastewaterTRUE           0.75     0.22     3.32   0.0004 
## ground_vegTRUE           1.07     0.24     4.43   0.0000 
## R1| R2                   1.28     0.55     2.32    0.01  
## R2| R3                   5.21     0.63     8.33      0   
## R3| R4                   10.67    0.78     13.71     0   
## ---------------------------------------------------------
par(mfrow=c(3,5))
plot.xmean.ordinaly (risk ~  building+ TC_mature_Soil+ DepTaludeAterro+  DepTaludeCorte+  construction_deposit+  crack+ leaning_wall+ scars+ downward_floor+ tilted+ conc_rainfall_water+ wastewater+ ground_veg
          ,data=train.data, cr=TRUE , subn=FALSE , cex.points =0.65)

sf <- function (y) {
        c('y>=1' = qlogis(mean(y>=1)),
          'y>=2' = qlogis(mean(y>=2)),
           'y>=3' = qlogis(mean(y>=3)),
            'y>=4' = qlogis(mean(y>=4)))
}

s<-with(train.data, summary(as.numeric(risk)~building+ TC_mature_Soil+ DepTaludeAterro+  DepTaludeCorte+  construction_deposit+  crack+ leaning_wall+ scars+ downward_floor+ tilted+ conc_rainfall_water+ wastewater+ ground_veg
, fun=sf))
s
## as.numeric(risk)     N= 529 
## 
## +--------------------+---+---+----+----------+-----------+-----------+
## |                    |   |N  |y>=1|y>=2      |y>=3       |y>=4       |
## +--------------------+---+---+----+----------+-----------+-----------+
## |building            |B  |459|Inf | 1.9139271|-0.22314355|-2.49438539|
## |                    |W  | 39|Inf | 2.4849066| 1.51982575|-0.05129329|
## |                    |M  | 31|Inf | 2.2335922| 1.05605267|-0.89381788|
## +--------------------+---+---+----+----------+-----------+-----------+
## |TC_mature_Soil      |No |274|Inf | 1.5493340|-0.32397207|-2.21355147|
## |                    |Yes|255|Inf | 2.6390573| 0.26028310|-1.80555279|
## +--------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeAterro     |No |510|Inf | 1.9236870|-0.10204925|-2.11296423|
## |                    |Yes| 19|Inf |       Inf| 2.14006616|-0.31845373|
## +--------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeCorte      |No |310|Inf | 1.5561934|-0.39204209|-2.47793798|
## |                    |Yes|219|Inf | 2.9396428| 0.45518854|-1.52939520|
## +--------------------+---+---+----+----------+-----------+-----------+
## |construction_deposit|No |322|Inf | 1.6244195|-0.45488999|-2.39113849|
## |                    |Yes|207|Inf | 2.7880929| 0.60738036|-1.55814462|
## +--------------------+---+---+----+----------+-----------+-----------+
## |crack               |No |444|Inf | 1.7812882|-0.40171276|-2.73724936|
## |                    |Yes| 85|Inf | 4.4308168| 3.00815479|-0.30830136|
## +--------------------+---+---+----+----------+-----------+-----------+
## |leaning_wall        |No |497|Inf | 1.8940383|-0.15726498|-2.23582188|
## |                    |Yes| 32|Inf |       Inf| 2.70805020|-0.12516314|
## +--------------------+---+---+----+----------+-----------+-----------+
## |scars               |No |322|Inf | 1.3746888|-1.55814462|-4.37575702|
## |                    |Yes|207|Inf |       Inf| 3.92691162|-0.91967483|
## +--------------------+---+---+----+----------+-----------+-----------+
## |downward_floor      |No |469|Inf | 1.8270276|-0.29639401|-2.45750768|
## |                    |Yes| 60|Inf |       Inf| 4.07753744|-0.26826399|
## +--------------------+---+---+----+----------+-----------+-----------+
## |tilted              |No |433|Inf | 1.7519136|-0.46550250|-2.59773918|
## |                    |Yes| 96|Inf | 4.5538769| 3.13549422|-0.64662716|
## +--------------------+---+---+----+----------+-----------+-----------+
## |conc_rainfall_water |No | 23|Inf |-1.0414539|       -Inf|       -Inf|
## |                    |Yes|506|Inf | 2.2556682| 0.04743973|-1.95043504|
## +--------------------+---+---+----+----------+-----------+-----------+
## |wastewater          |No |220|Inf | 1.3031440|-0.57931204|-3.04452244|
## |                    |Yes|309|Inf | 2.7829515| 0.33314445|-1.57488553|
## +--------------------+---+---+----+----------+-----------+-----------+
## |ground_veg          |No |162|Inf | 0.9249488|-1.36330484|-2.95751106|
## |                    |Yes|367|Inf | 2.9077635| 0.47177511|-1.73567000|
## +--------------------+---+---+----+----------+-----------+-----------+
## |Overall             |   |529|Inf | 1.9654973|-0.04159390|-2.00105091|
## +--------------------+---+---+----+----------+-----------+-----------+
plot(s, which=1:4, pch=1:4, xlab='logit', main=' ', xlim=c(-5,5), cex.lab=0.7, cex.axis=0.5, cex.sub=0.5)

OLR Equation 6

  • based on Equation 5 (less +construction_deposit, DepTaludeAterro )
  • p >0.5
# x=TRUE, y=TRUE used by resid() below 
#print (f1 , latex =TRUE , coefs =5)
#stargazer(anova(f1), type="text", style="default")

eq_OLR_06 <- polr(risk ~ building+ TC_mature_Soil+  DepTaludeCorte+  conc_rainfall_water +  crack+ leaning_wall+ scars+ downward_floor+ tilted + wastewater+ ground_veg,  data= train.data
           ,  method = "logistic", Hess = TRUE)

ctable <- coef(summary(eq_OLR_06))

p<- pnorm(abs(ctable[, "t value"]), lower.tail = FALSE*2) #computes p value
ctable <- cbind(ctable, "p value" = p )

ctable
##                              Value Std. Error   t value      p value
## building.L               0.0922464  0.3178444  0.290225 3.858220e-01
## building.Q              -0.9277081  0.3965392 -2.339512 9.654477e-03
## TC_mature_SoilTRUE       0.6469508  0.2214729  2.921129 1.743828e-03
## DepTaludeCorteTRUE       0.6100576  0.2222423  2.745011 3.025442e-03
## conc_rainfall_waterTRUE  1.9638250  0.5308624  3.699311 1.080927e-04
## crackTRUE                1.8446220  0.3315722  5.563258 1.323916e-08
## leaning_wallTRUE         1.5775416  0.4978685  3.168591 7.658989e-04
## scarsTRUE                4.2263787  0.4087253 10.340388 2.313291e-25
## downward_floorTRUE       1.5969674  0.3818416  4.182277 1.443021e-05
## tiltedTRUE               0.8892745  0.3202906  2.776461 2.747710e-03
## wastewaterTRUE           0.7493833  0.2239424  3.346322 4.094556e-04
## ground_vegTRUE           1.0689621  0.2404899  4.444935 4.395921e-06
## R1|R2                    1.2898202  0.5541111  2.327729 9.963262e-03
## R2|R3                    5.2148533  0.6245506  8.349769 3.419838e-17
## R3|R4                   10.6755386  0.7780199 13.721421 3.778476e-43
stargazer((ctable), type="text", style="default", digits = 2)
## 
## ========================================================
##                         Value Std. Error t value p value
## --------------------------------------------------------
## building.L              0.09     0.32     0.29    0.39  
## building.Q              -0.93    0.40     -2.34   0.01  
## TC_mature_SoilTRUE      0.65     0.22     2.92    0.002 
## DepTaludeCorteTRUE      0.61     0.22     2.75    0.003 
## conc_rainfall_waterTRUE 1.96     0.53     3.70   0.0001 
## crackTRUE               1.84     0.33     5.56      0   
## leaning_wallTRUE        1.58     0.50     3.17    0.001 
## scarsTRUE               4.23     0.41     10.34     0   
## downward_floorTRUE      1.60     0.38     4.18   0.0000 
## tiltedTRUE              0.89     0.32     2.78    0.003 
## wastewaterTRUE          0.75     0.22     3.35   0.0004 
## ground_vegTRUE          1.07     0.24     4.44   0.0000 
## R1| R2                  1.29     0.55     2.33    0.01  
## R2| R3                  5.21     0.62     8.35      0   
## R3| R4                  10.68    0.78     13.72     0   
## --------------------------------------------------------
par(mfrow=c(3,4))
plot.xmean.ordinaly (risk ~  building+ TC_mature_Soil+  DepTaludeCorte+  conc_rainfall_water +  crack+ leaning_wall+ scars+ downward_floor+ tilted + wastewater+ ground_veg
          ,data=train.data, cr=TRUE , subn=FALSE , cex.points =0.65)

sf <- function (y) {
        c('y>=1' = qlogis(mean(y>=1)),
          'y>=2' = qlogis(mean(y>=2)),
           'y>=3' = qlogis(mean(y>=3)),
            'y>=4' = qlogis(mean(y>=4)))
}

s<-with(train.data, summary(as.numeric(risk)~building+ TC_mature_Soil+  DepTaludeCorte+  conc_rainfall_water +  crack+ leaning_wall+ scars+ downward_floor+ tilted + wastewater+ ground_veg
, fun=sf))
s
## as.numeric(risk)     N= 529 
## 
## +-------------------+---+---+----+----------+-----------+-----------+
## |                   |   |N  |y>=1|y>=2      |y>=3       |y>=4       |
## +-------------------+---+---+----+----------+-----------+-----------+
## |building           |B  |459|Inf | 1.9139271|-0.22314355|-2.49438539|
## |                   |W  | 39|Inf | 2.4849066| 1.51982575|-0.05129329|
## |                   |M  | 31|Inf | 2.2335922| 1.05605267|-0.89381788|
## +-------------------+---+---+----+----------+-----------+-----------+
## |TC_mature_Soil     |No |274|Inf | 1.5493340|-0.32397207|-2.21355147|
## |                   |Yes|255|Inf | 2.6390573| 0.26028310|-1.80555279|
## +-------------------+---+---+----+----------+-----------+-----------+
## |DepTaludeCorte     |No |310|Inf | 1.5561934|-0.39204209|-2.47793798|
## |                   |Yes|219|Inf | 2.9396428| 0.45518854|-1.52939520|
## +-------------------+---+---+----+----------+-----------+-----------+
## |conc_rainfall_water|No | 23|Inf |-1.0414539|       -Inf|       -Inf|
## |                   |Yes|506|Inf | 2.2556682| 0.04743973|-1.95043504|
## +-------------------+---+---+----+----------+-----------+-----------+
## |crack              |No |444|Inf | 1.7812882|-0.40171276|-2.73724936|
## |                   |Yes| 85|Inf | 4.4308168| 3.00815479|-0.30830136|
## +-------------------+---+---+----+----------+-----------+-----------+
## |leaning_wall       |No |497|Inf | 1.8940383|-0.15726498|-2.23582188|
## |                   |Yes| 32|Inf |       Inf| 2.70805020|-0.12516314|
## +-------------------+---+---+----+----------+-----------+-----------+
## |scars              |No |322|Inf | 1.3746888|-1.55814462|-4.37575702|
## |                   |Yes|207|Inf |       Inf| 3.92691162|-0.91967483|
## +-------------------+---+---+----+----------+-----------+-----------+
## |downward_floor     |No |469|Inf | 1.8270276|-0.29639401|-2.45750768|
## |                   |Yes| 60|Inf |       Inf| 4.07753744|-0.26826399|
## +-------------------+---+---+----+----------+-----------+-----------+
## |tilted             |No |433|Inf | 1.7519136|-0.46550250|-2.59773918|
## |                   |Yes| 96|Inf | 4.5538769| 3.13549422|-0.64662716|
## +-------------------+---+---+----+----------+-----------+-----------+
## |wastewater         |No |220|Inf | 1.3031440|-0.57931204|-3.04452244|
## |                   |Yes|309|Inf | 2.7829515| 0.33314445|-1.57488553|
## +-------------------+---+---+----+----------+-----------+-----------+
## |ground_veg         |No |162|Inf | 0.9249488|-1.36330484|-2.95751106|
## |                   |Yes|367|Inf | 2.9077635| 0.47177511|-1.73567000|
## +-------------------+---+---+----+----------+-----------+-----------+
## |Overall            |   |529|Inf | 1.9654973|-0.04159390|-2.00105091|
## +-------------------+---+---+----+----------+-----------+-----------+
plot(s, which=1:4, pch=1:4, xlab='logit', main=' ', xlim=c(-5,5), cex.lab=0.7, cex.axis=0.5, cex.sub=0.5)

Equation 07

  • parameters okay and so/so
  • porportion
  • collinearity

f7 <- lrm(risk~options(contrasts=c(1,2,3), building)+ angle+EN+TC+ TC_mature_Soil+banana+TC_saprolito+ garbage+ landfill + construction_deposit + drainage + leak+ conc_rainfall_water+ crack+ tilted + leaning_wall + scars + tree + ground_veg , data= train.data, x=TRUE , y=TRUE) # x=TRUE, y=TRUE used by resid() below #print (f4 , latex =TRUE , coefs =5) stargazer(anova(f6), type=“text”, style=“default”)

eq_OLR_07 <- polr(risk~ angle+ building+ EN+ TC+ landfill+ garbage+ construction_deposit+ crack+ leaning_wall + scars+ tilted+ conc_rainfall_water+ leak+ tree+ wastewater+  ground_veg+  banana
                  , data= train.data
           ,  method = "logistic", Hess = TRUE)
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
p<- pnorm(abs(ctable[, "t value"]), lower.tail = FALSE*2) #computes p value

ctable <- coef(summary(eq_OLR_07))

ctable <- cbind(ctable, "p value" = p )
## Warning in cbind(ctable, `p value` = p): number of rows of result is not a
## multiple of vector length (arg 2)
ctable
##                                 Value Std. Error     t value      p value
## angleB                   -0.913706215  1.5019548 -0.60834468 3.858220e-01
## angleC                    0.223772028  1.4847154  0.15071712 9.654477e-03
## angleD                    0.776051365  1.4803118  0.52424857 1.743828e-03
## angleE                    1.698879667  1.4946733  1.13662278 3.025442e-03
## building.L                0.315444587  0.3201773  0.98521836 1.080927e-04
## building.Q               -0.779608789  0.3861476 -2.01893967 1.323916e-08
## ENTRUE                    0.416799545  0.2845248  1.46489725 7.658989e-04
## TCTRUE                    1.013541004  0.4077912  2.48544081 2.313291e-25
## landfillTRUE              0.353984781  0.2493409  1.41968191 1.443021e-05
## garbageTRUE               0.499703046  0.3507553  1.42464878 2.747710e-03
## construction_depositTRUE  0.034017604  0.3392781  0.10026465 4.094556e-04
## crackTRUE                 1.633402258  0.3374018  4.84111903 4.395921e-06
## leaning_wallTRUE          1.481760119  0.4912784  3.01613098 9.963262e-03
## scarsTRUE                 4.411552419  0.4177655 10.55987643 3.419838e-17
## tiltedTRUE                0.946739751  0.3260472  2.90368911 3.778476e-43
## conc_rainfall_waterTRUE   1.830024475  0.5871908  3.11657555 3.858220e-01
## leakTRUE                  0.110519544  0.2370412  0.46624622 9.654477e-03
## treeTRUE                 -0.035690236  0.2457197 -0.14524774 1.743828e-03
## wastewaterTRUE            0.818820842  0.2322368  3.52580170 3.025442e-03
## ground_vegTRUE            0.756267159  0.2683732  2.81796819 1.080927e-04
## bananaTRUE                0.005044643  0.2627487  0.01919949 1.323916e-08
## R1|R2                     2.175030159  1.5678979  1.38722692 7.658989e-04
## R2|R3                     6.352307282  1.6038661  3.96062205 2.313291e-25
## R3|R4                    11.809412362  1.6839692  7.01284344 1.443021e-05
stargazer((ctable), type="text", style="default", digits = 2)
## 
## =========================================================
##                          Value Std. Error t value p value
## ---------------------------------------------------------
## angleB                   -0.91    1.50     -0.61   0.39  
## angleC                   0.22     1.48     0.15    0.01  
## angleD                   0.78     1.48     0.52    0.002 
## angleE                   1.70     1.49     1.14    0.003 
## building.L               0.32     0.32     0.99   0.0001 
## building.Q               -0.78    0.39     -2.02     0   
## ENTRUE                   0.42     0.28     1.46    0.001 
## TCTRUE                   1.01     0.41     2.49      0   
## landfillTRUE             0.35     0.25     1.42   0.0000 
## garbageTRUE              0.50     0.35     1.42    0.003 
## construction_depositTRUE 0.03     0.34     0.10   0.0004 
## crackTRUE                1.63     0.34     4.84   0.0000 
## leaning_wallTRUE         1.48     0.49     3.02    0.01  
## scarsTRUE                4.41     0.42     10.56     0   
## tiltedTRUE               0.95     0.33     2.90      0   
## conc_rainfall_waterTRUE  1.83     0.59     3.12    0.39  
## leakTRUE                 0.11     0.24     0.47    0.01  
## treeTRUE                 -0.04    0.25     -0.15   0.002 
## wastewaterTRUE           0.82     0.23     3.53    0.003 
## ground_vegTRUE           0.76     0.27     2.82   0.0001 
## bananaTRUE               0.01     0.26     0.02      0   
## R1| R2                   2.18     1.57     1.39    0.001 
## R2| R3                   6.35     1.60     3.96      0   
## R3| R4                   11.81    1.68     7.01   0.0000 
## ---------------------------------------------------------
par(mfrow=c(5,4))
plot.xmean.ordinaly (risk ~   building+ angle+ EN+ TC+ landfill+ garbage+ banana+ leak+ conc_rainfall_water+  tree+ wastewater+ scars+ tilted+ ground_veg+ construction_deposit+ crack+ leaning_wall
          ,data=train.data, cr=TRUE , subn=FALSE , cex.points =0.65)

sf <- function (y) {
        c('y>=1' = qlogis(mean(y>=1)),
          'y>=2' = qlogis(mean(y>=2)),
           'y>=3' = qlogis(mean(y>=3)),
            'y>=4' = qlogis(mean(y>=4)))
}

s<-with(train.data, summary(as.numeric(risk)~ building+ angle+ EN+ TC+ landfill+ garbage+ banana+ leak+ conc_rainfall_water+  tree+ wastewater+ scars+ tilted+ ground_veg+ construction_deposit+ crack+ leaning_wall
, fun=sf))
s
## as.numeric(risk)     N= 529 
## 
## +--------------------+---+---+----+----------+-----------+-----------+
## |                    |   |N  |y>=1|y>=2      |y>=3       |y>=4       |
## +--------------------+---+---+----+----------+-----------+-----------+
## |building            |B  |459|Inf | 1.9139271|-0.22314355|-2.49438539|
## |                    |W  | 39|Inf | 2.4849066| 1.51982575|-0.05129329|
## |                    |M  | 31|Inf | 2.2335922| 1.05605267|-0.89381788|
## +--------------------+---+---+----+----------+-----------+-----------+
## |angle               |A  |  3|Inf | 0.6931472|       -Inf|       -Inf|
## |                    |B  | 46|Inf |-0.3513979|-1.89711998|-3.80666249|
## |                    |C  | 82|Inf | 1.6691571|-1.00330211|-3.27083556|
## |                    |D  |293|Inf | 2.6137395| 0.33764251|-1.84451003|
## |                    |E  |105|Inf | 3.2288262| 0.28768207|-1.50990832|
## +--------------------+---+---+----+----------+-----------+-----------+
## |EN                  |No |348|Inf | 1.5288574|-0.50470003|-2.51645501|
## |                    |Yes|181|Inf | 4.0831713| 0.88173835|-1.35889539|
## +--------------------+---+---+----+----------+-----------+-----------+
## |TC                  |No | 46|Inf | 0.6286087|-0.17435339|-1.41369334|
## |                    |Yes|483|Inf | 2.1812242|-0.02898754|-2.07247287|
## +--------------------+---+---+----+----------+-----------+-----------+
## |landfill            |No |331|Inf | 1.5490288|-0.57746278|-2.74406064|
## |                    |Yes|198|Inf | 3.3063633| 0.88119941|-1.28222500|
## +--------------------+---+---+----+----------+-----------+-----------+
## |garbage             |No |355|Inf | 1.7181262|-0.33550652|-2.53796121|
## |                    |Yes|174|Inf | 2.6958549| 0.56639547|-1.30906301|
## +--------------------+---+---+----+----------+-----------+-----------+
## |banana              |No |363|Inf | 1.5995532|-0.40776132|-2.23766555|
## |                    |Yes|166|Inf | 3.7013020| 0.78495473|-1.59504917|
## +--------------------+---+---+----+----------+-----------+-----------+
## |leak                |No |345|Inf | 1.6625477|-0.35737892|-2.59338729|
## |                    |Yes|184|Inf | 2.8564702| 0.55748132|-1.31317210|
## +--------------------+---+---+----+----------+-----------+-----------+
## |conc_rainfall_water |No | 23|Inf |-1.0414539|       -Inf|       -Inf|
## |                    |Yes|506|Inf | 2.2556682| 0.04743973|-1.95043504|
## +--------------------+---+---+----+----------+-----------+-----------+
## |tree                |No |223|Inf | 1.3475083|-0.67972416|-2.37368101|
## |                    |Yes|306|Inf | 2.7150432| 0.41091471|-1.78415487|
## +--------------------+---+---+----+----------+-----------+-----------+
## |wastewater          |No |220|Inf | 1.3031440|-0.57931204|-3.04452244|
## |                    |Yes|309|Inf | 2.7829515| 0.33314445|-1.57488553|
## +--------------------+---+---+----+----------+-----------+-----------+
## |scars               |No |322|Inf | 1.3746888|-1.55814462|-4.37575702|
## |                    |Yes|207|Inf |       Inf| 3.92691162|-0.91967483|
## +--------------------+---+---+----+----------+-----------+-----------+
## |tilted              |No |433|Inf | 1.7519136|-0.46550250|-2.59773918|
## |                    |Yes| 96|Inf | 4.5538769| 3.13549422|-0.64662716|
## +--------------------+---+---+----+----------+-----------+-----------+
## |ground_veg          |No |162|Inf | 0.9249488|-1.36330484|-2.95751106|
## |                    |Yes|367|Inf | 2.9077635| 0.47177511|-1.73567000|
## +--------------------+---+---+----+----------+-----------+-----------+
## |construction_deposit|No |322|Inf | 1.6244195|-0.45488999|-2.39113849|
## |                    |Yes|207|Inf | 2.7880929| 0.60738036|-1.55814462|
## +--------------------+---+---+----+----------+-----------+-----------+
## |crack               |No |444|Inf | 1.7812882|-0.40171276|-2.73724936|
## |                    |Yes| 85|Inf | 4.4308168| 3.00815479|-0.30830136|
## +--------------------+---+---+----+----------+-----------+-----------+
## |leaning_wall        |No |497|Inf | 1.8940383|-0.15726498|-2.23582188|
## |                    |Yes| 32|Inf |       Inf| 2.70805020|-0.12516314|
## +--------------------+---+---+----+----------+-----------+-----------+
## |Overall             |   |529|Inf | 1.9654973|-0.04159390|-2.00105091|
## +--------------------+---+---+----+----------+-----------+-----------+
plot(s, which=1:4, pch=1:4, xlab='logit', main=' ', xlim=c(-5,5), cex.lab=0.7, cex.axis=0.5, cex.sub=0.5)

Predicion on test data Eq 1: http://r-statistics.co/Ordinal-Logistic-Regression-With-R.html

predictedLevel1 <- predict(eq_OLR_01, test.data) # predict the levels directly

predictedScores1 <- predict(eq_OLR_01, test.data, type="p") 
 # predict the probabilites

## Confusion matrix and misclassification error
table(test.data$risk, predictedLevel1)
##     predictedLevel1
##      R1 R2 R3 R4
##   R1  5 21  1  0
##   R2  2 78  7  0
##   R3  0 20 52 11
##   R4  0  1 17  9
p1 <- mean(as.character(test.data$risk) != as.character(predictedLevel1)) #misclassification error
p1 
## [1] 0.3571429

Predicion on test data Eq 2: http://r-statistics.co/Ordinal-Logistic-Regression-With-R.html

predictedLevel2 <- predict(eq_OLR_02, test.data) # predict the levels directly

## Confusion matrix and misclassification error
table(test.data$risk, predictedLevel2)
##     predictedLevel2
##      R1 R2 R3 R4
##   R1 15 11  1  0
##   R2  7 75  5  0
##   R3  0 21 55  7
##   R4  0  1 16 10
p2 <- mean(as.character(test.data$risk) != as.character(predictedLevel2))
p2
## [1] 0.3080357

Predicion on test data Eq 3: http://r-statistics.co/Ordinal-Logistic-Regression-With-R.html

predictedLevel3 <- predict(eq_OLR_03, test.data) # predict the levels directly

predictedScores1 <- predict(eq_OLR_03, test.data, type="p") 
 # predict the probabilites

## Confusion matrix and misclassification error
table(test.data$risk, predictedLevel3)
##     predictedLevel3
##      R1 R2 R3 R4
##   R1  6 20  1  0
##   R2  2 76  9  0
##   R3  0 18 57  8
##   R4  0  1 16 10
p3 <- mean(as.character(test.data$risk) != as.character(predictedLevel3))
p3
## [1] 0.3348214

Predicion on test data Eq 4: http://r-statistics.co/Ordinal-Logistic-Regression-With-R.html

predictedLevel4 <- predict(eq_OLR_04, test.data) # predict the levels directly

predictedScores1 <- predict(eq_OLR_04, test.data, type="p") 
 # predict the probabilites

## Confusion matrix and misclassification error
table(test.data$risk, predictedLevel4)
##     predictedLevel4
##      R1 R2 R3 R4
##   R1  6 20  1  0
##   R2  2 78  7  0
##   R3  0 19 57  7
##   R4  0  1 16 10
p4 <- mean(as.character(test.data$risk) != as.character(predictedLevel4))
p4
## [1] 0.3258929

Predicion on test data Eq 5: http://r-statistics.co/Ordinal-Logistic-Regression-With-R.html

predictedLevel5 <- predict(eq_OLR_05, test.data) # predict the levels directly

predictedScores5 <- predict(eq_OLR_05, test.data, type="p") 
 # predict the probabilites

## Confusion matrix and misclassification error
table(test.data$risk, predictedLevel5)
##     predictedLevel5
##      R1 R2 R3 R4
##   R1  5 21  1  0
##   R2  2 78  7  0
##   R3  0 19 57  7
##   R4  0  1 17  9
p5 <- mean(as.character(test.data$risk) != as.character(predictedLevel5))
p5
## [1] 0.3348214

Predicion on test data Eq 6: http://r-statistics.co/Ordinal-Logistic-Regression-With-R.html

predictedLevel6 <- predict(eq_OLR_06, test.data) # predict the levels directly

predictedScores6 <- predict(eq_OLR_06, test.data, type="p") 
 # predict the probabilites

## Confusion matrix and misclassification error
table(test.data$risk, predictedLevel6)
##     predictedLevel6
##      R1 R2 R3 R4
##   R1  5 21  1  0
##   R2  2 78  7  0
##   R3  0 20 56  7
##   R4  0  1 17  9
p6 <- mean(as.character(test.data$risk) != as.character(predictedLevel6))
p6
## [1] 0.3392857

Predicion on test data Eq 7: http://r-statistics.co/Ordinal-Logistic-Regression-With-R.html

predictedLevel7 <- predict(eq_OLR_07, test.data) # predict the levels directly

predictedScores7 <- predict(eq_OLR_07, test.data, type="p") 
 # predict the probabilites

## Confusion matrix and misclassification error
table(test.data$risk, predictedLevel7)
##     predictedLevel7
##      R1 R2 R3 R4
##   R1 14 12  1  0
##   R2  7 74  6  0
##   R3  0 23 57  3
##   R4  0  1 17  9
p7 <- mean(as.character(test.data$risk) != as.character(predictedLevel7))
p7
## [1] 0.3125
#Table 

df2 <- data.frame(
  
  "Equations"=c(1:7), 
  "Predicted"=c(1-p1, 
                1-p2,
                1-p3,
                1-p4,
                1-p5,
                1-p6,
                1-p7
              
    
    
  )
  
  
  
)

df2
##   Equations Predicted
## 1         1 0.6428571
## 2         2 0.6919643
## 3         3 0.6651786
## 4         4 0.6741071
## 5         5 0.6651786
## 6         6 0.6607143
## 7         7 0.6875000